From: Axel Kohlmeyer (
Date: Sun Feb 20 2011 - 09:42:19 CST


On Sun, Feb 20, 2011 at 8:54 AM, Sebastian Wilhelm
<> wrote:
> Hi,
> I have an error occurring while using Auto PSF Builder: the coordinates of
> 100 simple argon molecules which I simulated by DL POLY are converted by VMD

argon is not a molecule but an atomic noble gas.

> to a .pdb-file. Loading them and the topology file
> top_all27_prot_lipid_na.inp into Auto PSF Builder and choosing 'everything'
> in step 2, in step 3 only one chain segment is presented which has a first
> atom number of 1 and a last atom number of 101 (to be found in ‘edit
> chains’). Clicking on ‘create chains’ produces an application error ‘ERROR:
> failed on end of segment MOLECULE DESTROYED BY FATAL ERROR’. In the command
> box, there is written ‘unknown residue type’.

yes. because it is the _automatic_ psf builder, not the _magic_ psf builder.
it can only generate psf files for compounds that it knows and is trained to
handle, and that means for the most part biomolecules.

for argon you don't really have to run through autopsf.

just look up in the parameter file, which atom type would
correspond to argon, load your .pdb file and then execute a
few script statements on the VMD console.

set sel [atomselect top all]
$sel set {type mass charge resname} {AR 39.948 0.0 AR}
$sel set resid [$sel get serial]

animate write psf argon.psf waitfor all

that should do. you have to adjust the atom type as needed, of course.


> My goal is to calculate all intermolecular energies by NAMDenergy for that I
> need a .psf-file.
> What can I do? Do I have to change the topology file, and when how?
> Thanks for your help.
> Best regards,
> Sebastian Wilhelm

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.